Mercurial > repos > iuc > bcftools_convert_to_vcf

annotate test-data/query.vcf @ 15:de68c11034f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70
author iuc
date Sat, 23 Jul 2022 13:46:32 +0000
parents b068ef999550
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 ##fileformat=VCFv4.1
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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9 ##FILTER=<ID=q10,Description="Quality below 10">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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10 ##FILTER=<ID=test,Description="Testing filter">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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11 ##contig=<ID=1,assembly=b37,length=249250621>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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12 ##contig=<ID=3,assembly=b37,length=198022430>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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13 ##contig=<ID=4,assembly=b37,length=191154276>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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14 ##contig=<ID=2,assembly=b37,length=249250621>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 ##readme=AAAAAA
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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17 ##readme=BBBBBB
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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19 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT C D
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 1 3062915 id3D GTTT G 48.7 q10 DP4=1,2,3,4;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:109:25:-10,-5,-20
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 1 3062915 idSNP G C,T 419 test TEST=5;DP4=1,2,3,4;AN=4;AC=1,1 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 0/2:0,1:109:35:-10,-5,-20,-20,-5,-20
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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23 1 3062915 id2D GTT G 999 q10 DP4=1,2,3,4;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:109:25:-10,-5,-20
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 1 3106154 . CAAA C 72.6 PASS AN=0;AC=0 GT:GQ:DP .:245:32 ./.:145:22
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 1 3106154 . C CT 459 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:145:22
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 1 3157410 . G T 46.7 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:11:11
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 1 3162006 . GAA G 206 PASS AN=4;AC=2 GT:GQ:DP 0/1:212:22 0/1:112:12
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 1 3177144 . G . 364 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:20
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 1 3184885 . TAAAA TA,T 8.42 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:22:20 1/2:12:10
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 2 3199812 . G GTT,GT 291 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:122:16
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 3 3212016 . CTT C,CT 52.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:11:16
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 4 3258448 . TACACACAC T 123 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:125:11
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 4 3258449 . A C 123 PASS AN=4;AC=3 GT:GQ:DP 1/1:325:31 0/1:125:11